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Series GSE220891 Query DataSets for GSE220891
Status Public on Dec 14, 2022
Title Genomic landscapes of ovarian clear cell carcinoma from Latin countries reveal aberrations linked to survival and progression
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Background: Ovarian clear cell carcinomas (OCCCs) are rare, aggressive and chemoresistant tumors. Geographical and ethnic differences in the incidence of OCCC have been reported with a higher incidence in Asiatic countries. There is a paucity of information regarding OCCC in Latin America (LA) and other countries.

Methods: Here, we characterized two cohorts of 33 patients with OCCC from LA (24 from Brazil and 9 from Costa Rica) and a cohort of 27 patients from Spain. Genomic analysis was performed for 26 OCCC using the OncoScan platform. Tumors were classified according to their genomic landscapes into subgroups. Clinical parameters were related to the frequency of genomic aberrations.

Results: The median overall survival (OS) was not significantly different between the cohorts. Genomic landscapes were characterized by different homologous recombination deficiency (HRD) levels. No difference in the distribution of genomic landscapes profiles was detected between patients from the different cohorts. OCCCs with MYC-amplified tumors harboring a concomitant loss of a region in chromosome 13q12-q13 that includes the BRCA2 gene had the longest OS. In contrast, patients carrying a high number (> 30) of total copy number (CN) aberrations with no concomitant alterations in MYC and BRCA2 genes presented the shortest OS. Furthermore, amplification of the ASH1L gene was also associated with a shorter OS. Initial-stage OCCCs with early progression were characterized by gains in the JNK1 and MKL1 genes.

Conclusions: Our results provide new data from understudied OCCC populations and reveal new potential markers for OCCCs.
 
Overall design Sixty patients older than 18 years old with a histological diagnosis of OCCC between 2000 and 2015 were recruited from institutions in three different countries: 7 patients from Hospital das Clínicas de Ribeirão Preto (HCRP) - Brazil; 17 patients from A.C.Camargo Cancer Center (ACCCC) - Brazil; 9 patients from Hospital México (HM) – Costa Rica; and 27 patients from Instituto Valenciano de Oncología (IVO) – Spain. Fifty-seven samples were obtained from the primary tumor, and 4 corresponded to metastatic tissue after recurrence. The samples were reviewed by two pathologists to confirm the diagnosis of pure OCCC histology. DNA extracted from 26 primary tumors and one recurrent tumor was subjected to the SNP array OncoScan® FFPE (Thermo)
 
Contributor(s) de Paiva Batista M, Roffe M, Rego EM
Citation(s) 37400764
Submission date Dec 13, 2022
Last update date Jul 26, 2023
Contact name Martin - Roffe
E-mail(s) MRoffe@cheo.on.ca
Organization name CHEO Research Institute
Street address 401 Smyth Rd
City Ottawa
State/province ON
ZIP/Postal code K1H 5B2
Country Canada
 
Platforms (1)
GPL21558 [OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay
Samples (27)
GSM6825556 Ovarian Clear Cell Carcinoma 1
GSM6825557 Ovarian Clear Cell Carcinoma 2
GSM6825558 Ovarian Clear Cell Carcinoma 4
Relations
BioProject PRJNA911812

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE220891_BAF.txt.gz 19.3 Mb (ftp)(http) TXT
GSE220891_RAW.tar 651.8 Mb (http)(custom) TAR (of CEL, OSCHP)
GSE220891_allelic_difference.txt.gz 24.5 Mb (ftp)(http) TXT
GSE220891_weighted_log2_ratio.txt.gz 25.6 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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